Although the Santa Clara County Office of Education has accepted responsibility for filing its taxes late, it’s getting a $174,000 refund of a penalty it paid the Internal Revenue Service.

In its March appeal letter, the County Office of Education blamed the Santa Clara County Controller-Treasurer for the delayed remittance of payroll taxes, and insisted that taxes had always been filed on time.

But by their own admission and according to documents, neither of those claims were true.

For years, the education office itself has electronically transferred funds to the IRS for federal payroll taxes. In September 2010, it filed its taxes a day after the due date. Last fall, the IRS assessed a $174,000 penalty and also imposed fines for other late taxes.

Micaela Ochoa, the education office’s chief business officer, refused to return phone calls about the tax payments. However, in an emailed statement, she wrote that tracing the payment was difficult and documentation was confusing. She also noted that the delinquent payment preceded her joining the education office in August 2012.

However, last year the IRS assessed the office a $3.18 million penalty for delinquent taxes, an amount later knocked down to $6,500. The office paid most of the late-payment penalties, but appealed the largest one.

After this newspaper inquired about claims in the March appeal letter, the education office conceded that it was responsible for paying payroll taxes. Spokesman Ken Blackstone blamed the claims in the letter on a director of payroll, who has since left the office.

Emily Harrison, Santa Clara County director of finance, said she discussed the tax payments with Ochoa and her staff earlier this year. “It became clear that the staff was afraid of being tagged with a mistake, but finally admitted they were late,” Harrison said.

IRS spokesman Raphael Tulino, citing a policy of not commenting on specific cases, declined to comment.

The education office’s March appeal claimed, “We have a 164-year history of filing accurate and timely payroll tax returns,” even though it missed the deadline for two periods earlier in 2010.

The tax payments cover payroll taxes for employees of the education office and 27 of the county’s 31 school districts, from Palo Alto to Gilroy. On the appeal of September 2010 taxes, the IRS refunded the $174,091 penalty, plus $659 in previously charged interest and $1,428 in additional interest accrued on the penalty that was paid.

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